As the SAM/BAM spec says:
Note that tags starting with ‘X’, ‘Y’ and ‘Z’ or tags containing lowercase letters in either position are reserved for local use and will not be formally defined in any future version of this specification.
These optional tags are used by all sorts of aligners and downstream programs. Some of them are so prevalent (like XM) that they are just as well known as the official tags.
After some interesting discussion on Remove optical duplicates from bam file, I am thinking it would be pretty neat to have an "optical duplicate" tag, and/or a PCR duplicate and biological duplicate tag, to differentiate between the three. Currently the flag 010000000000 is being used for duplicates, but it doesn't differentiate between the three.
So before I modify Anna's script (from the above thread) to tag reads rather than delete them, I'm wondering if there is a list of know or common user-tags out there that I can check against, so i choose a new one not an existing one. Probably I would choose XO (optical), XP (PCR), XB (Biological) -- but one or all might already be taken! :)